A Shiny App for R-Package Risk Assessment

Lars Andersen, 21st July 2023 @useR! 2023 Basel

Disclaimer




Any opinions expressed in this presentation and on the following slides are solely those of the presenter and do not necessarily reflect those sponsoring the work

Validating open-source software

[Add big RVal Hub logo]

  • Group of ~50 companies (mostly pharma & biotech)


  • Mission: R Validation Hub is a cross-industry initiative whose mission is to enable the use of R by the Bio-Pharmaceutical industry in a regulatory setting, where the output may be used in submissions to regulatory agencies.

Two tools: what do they do



is a framework to quantify an R package’s “risk” by assessing several meaningful metrics designed to evaluate package development best practices, code documentation, community engagement, and development sustainability.


is a full-fledged R package containing a shiny front-end that augments the utility of {riskmetric}. The application’s goal is to provide a central hub for an organization to review and assess the risk of R packages, providing handy tools and guide rails along the way.

Two tools: where they fit

Quantify risk programmatically

Sometimes “quality” is measurable! Software dev best practices dictate an R-package should have:

  • A license
  • Source code available for browsing
  • An easy to contact maintainer
  • A place to report bugs
  • Evidence that new bugs are being addressed
  • Complete Function documentation
  • Adequate test coverage
  • Community usage

18 total assessments (to date)!

Why create a Shiny app?

Our audience / users: those those making ‘package inclusion’ requests for GxP environments. They need support to…

  • Generate consistent, org-specific analysis of risk outputs & a means for package exploration without the need to write R code
  • Run {riskmetric} on the same machine with the same environment – creating a central hub for reproducibility
  • Automate ‘decision triage’ based on pre-defined rules, saving time & mental energy
  • Manage who’s involved in the review process with user authentication with user role management
  • Facilitate and store communication between many users, on certain packages and/or metrics
  • Generate risk summary reports, with opportunity to inject opinions, for sharing with the decision making parties

Today: latest features

Demo




Shinyapps.io

Coming soon

{riskscore}

In it’s early stages, a new data package containing the {riskmetric} assessments & scores for all packages on CRAN.

Coming soon

Package Explorer

A suite of hands-on review tools (from our friends at GSK) will allow users to browse unit tests, source code, and man (doc) pages for any exported function.

Dev Team

Q & A